Zinc in PDB 5i4j: DPS4 From Nostoc Punctiforme in Complex with Zn Ions

The structure of DPS4 From Nostoc Punctiforme in Complex with Zn Ions, PDB code: 5i4j was solved by C.Howe, V.K.Moparthi, K.Persson, K.Stensjo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.39
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	100.920, 100.920, 144.270, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 21.4

The binding sites of Zinc atom in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions (pdb code 5i4j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions, PDB code: 5i4j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DPS4 From Nostoc Punctiforme in Complex with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:74.2 occ:0.72 NE2 A:HIS78 2.3 63.8 1.0 NE2 B:HIS51 2.4 48.2 1.0 OE1 A:GLU82 2.5 75.6 1.0 CE1 A:HIS78 2.6 64.1 1.0 CD A:GLU82 3.1 70.4 1.0 CE1 B:HIS51 3.1 45.0 1.0 OE2 A:GLU82 3.5 74.7 1.0 CD2 B:HIS51 3.6 45.1 1.0 CD2 A:HIS78 3.6 60.6 1.0 ND1 A:HIS78 3.8 62.0 1.0 CE1 B:HIS63 3.8 61.5 1.0 NE2 B:HIS63 3.9 59.7 1.0 CG A:GLU82 4.1 57.5 1.0 ND2 B:ASN67 4.3 59.8 1.0 CG A:HIS78 4.3 55.8 1.0 ND1 B:HIS51 4.4 45.8 1.0 CG B:HIS51 4.6 43.4 1.0 ND1 B:HIS63 4.8 57.9 1.0 CD2 B:HIS63 4.9 53.5 1.0

Zinc binding site 2 out of 4 in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DPS4 From Nostoc Punctiforme in Complex with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:81.4 occ:0.59 OE2 B:GLU82 2.1 70.2 1.0 NE2 B:HIS78 2.3 65.1 1.0 NE2 A:HIS51 2.4 51.6 1.0 CE1 B:HIS78 2.7 64.3 1.0 CE1 A:HIS51 3.0 51.4 1.0 CD B:GLU82 3.2 70.4 1.0 NE2 A:HIS63 3.6 64.8 1.0 CD2 B:HIS78 3.6 62.2 1.0 CD2 A:HIS51 3.6 54.4 1.0 OE1 B:GLU82 3.7 75.5 1.0 ND1 B:HIS78 4.0 61.3 1.0 CE1 A:HIS63 4.1 64.2 1.0 ND1 A:HIS51 4.2 52.8 1.0 CG B:GLU82 4.5 61.2 1.0 CG B:HIS78 4.5 58.0 1.0 CD2 A:HIS63 4.6 60.6 1.0 CG A:HIS51 4.6 55.1 1.0 OD1 A:ASN67 4.6 62.0 1.0

Zinc binding site 3 out of 4 in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DPS4 From Nostoc Punctiforme in Complex with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:75.7 occ:0.71 NE2 C:HIS78 2.2 63.4 1.0 CE1 C:HIS78 2.4 68.3 1.0 NE2 D:HIS51 2.5 46.8 1.0 OE2 C:GLU82 2.6 83.7 1.0 O C:HOH306 2.8 61.9 1.0 CE1 D:HIS51 3.2 49.1 1.0 CD C:GLU82 3.4 80.8 1.0 OE1 C:GLU82 3.4 82.7 1.0 CD2 C:HIS78 3.4 65.6 1.0 CD2 D:HIS51 3.6 51.8 1.0 ND1 C:HIS78 3.7 69.8 1.0 NE2 D:HIS63 3.8 68.6 1.0 CE1 D:HIS63 3.9 69.7 1.0 CG C:HIS78 4.2 64.5 1.0 ND1 D:HIS51 4.4 52.0 1.0 CG D:HIS51 4.6 52.0 1.0 CG C:GLU82 4.8 71.6 1.0 CD2 D:HIS63 4.9 66.8 1.0 ND1 D:HIS63 5.0 67.0 1.0

Zinc binding site 4 out of 4 in the DPS4 From Nostoc Punctiforme in Complex with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DPS4 From Nostoc Punctiforme in Complex with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:77.0 occ:0.69 NE2 D:HIS78 2.2 62.0 1.0 NE2 C:HIS51 2.4 52.0 1.0 CE1 D:HIS78 2.5 62.8 1.0 O D:HOH310 2.9 62.4 1.0 CE1 C:HIS51 3.2 49.6 1.0 OE2 D:GLU82 3.2 78.4 1.0 CD D:GLU82 3.3 76.6 1.0 OE1 D:GLU82 3.4 81.8 1.0 CD2 C:HIS51 3.5 52.0 1.0 CD2 D:HIS78 3.6 62.6 1.0 NE2 C:HIS63 3.7 62.6 1.0 ND1 D:HIS78 3.8 62.7 1.0 CE1 C:HIS63 4.0 59.2 1.0 CG D:GLU82 4.1 68.6 1.0 CG D:HIS78 4.3 60.5 1.0 ND1 C:HIS51 4.4 53.2 1.0 OD1 C:ASN67 4.6 64.9 1.0 CG C:HIS51 4.6 52.3 1.0 CD2 C:HIS63 4.7 62.0 1.0

C.Howe, V.K.Moparthi, K.Persson, K.Stensjo. On the Trail of Iron Into DPS4 From N. Punctiforme To Be Published.